I'm not certain from the question about what "doneness" means. Is the bread still "raw" inside at 95C? If so, I'd guess something is wrong with the calibration of the thermometer.
Failing that, my guess is that this has to do with either various other external factors (e.g., the bread may be "set" inside, but the exterior is not browned sufficiently, or the crust dried out enough) and/or things having to do with moisture.
Once you get to 95C and above, the structure of the bread is definitely set. It's not going to collapse if you pull it out of the oven. It shouldn't taste "raw" or overly "doughy" inside. The bread should be "done," at least in the sense of fully cooked.
But to my point about moisture: what generally happens to bread once it reaches a high internal temperature is that the internal structure gradually dries out. It takes a long time for moisture to migrate out from the center and through the increasingly hard crust. The interior of the bread will change from a spongy and "moist" texture to an increasingly dry and stiff one as time elapses in the oven. The retained moisture when the bread is pulled from the oven also can have significant effects on the outcome: a dough that is very moist before bake and which doesn't expand much will often remain moist internally, and that moisture will likely rebalance itself during cooling, some of it going to the crust, which will soften. If you want a crisp crust, you'll have to bake longer.
Some of it may have to do with the recipe. For example, a quick hot bake may give good oven spring, but may not allow sufficient time for moisture migration. So a crusty bread baked too fast may display a high internal temp, but then soften as it cools. Turning the temperature down during the bake may allow for the desired texture with a longer bake (and without burning the exterior). If your bake time is off from the recipe, the internal temperature may not be as reliable an indicator.
Some of it may have to do with loaf and dough characteristics. As hinted above, oven spring and size of holes inside the interior plays a significant role in how moisture migrates internally. If your bread isn't rising as much as the recipe assumes (or rising too much), you might need to change your bake time/temp as well as your assumed final interior temperature for the loaf. Extra humidity absorbed or lost due to kitchen conditions at different times of the year can also play a role -- I've baked the same recipe under different humidity and temperature conditions with precise measurements and gotten significantly different results.
Lastly, of course your personal taste concerning doneness may vary from the person who wrote the recipe. Sourdough breads can vary inside from everything from a kind of "creamy" and somewhat moist interior to a very dry and tough/chewy interior. Personally, I like the former, but if you like the latter, maybe you are most satisfied with a result different from the one the recipe intended.
Bottom line is that internal temp is a guideline just like anything else. But I personally have found it more useful than other guidelines (like the "hollow sound" test, browning level of exterior). You may need to tweak according to your own experience and preferences.